ENH: Add a GenerateCLP command line for GenerateAverageLmkFile

Usage:
$/GenerateAverageLmkFile \
--inputLandmarkFiles lmk1.fcsv,lmk2.fcsv,...,lmkn.fcsv \
--outputLandmarkFile outputAveLmk.fcsv
ENH: Removed unnecessary code.
WIP: FIXING BUGS IN template use for phase 3.
WIP: Reorganize pipeline to be consistent

The process of building the pipeline sould
be contained in one set of files, not distributed
across several files somewhat indeterminantly..
WIP: Fixed cross sectional bugs in refactoring.
WIP: More changes for BAW debugging.